Mercurial > repos > tomnl > mspurity_averagefragspectra

comparison averageFragSpectra.xml @ 15:42bfb67c3b62 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:33:15 +0000
parents e0b1da3ed06b
children
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14:1f74d9d92834 15:42bfb67c3b62
1 <tool id="mspurity_averagefragspectra" name="msPurity.averageFragSpectra" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@"> 1 <tool id="mspurity_averagefragspectra" name="msPurity.averageFragSpectra" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description> 2 <description>Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All)</description>
3 Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All)
4 </description>
5
6 <macros> 3 <macros>
7 <import>macros.xml</import> 4 <import>macros.xml</import>
8 </macros> 5 </macros>
9 6 <expand macro="requirements"/>
10 <expand macro="requirements"> 7 <command detect_errors="exit_code"><![CDATA[
11 </expand> 8 Rscript '$__tool_directory__/averageFragSpectra.R'
12 9 --out_rdata='$averageFragSpectra_output_rdata'
13 <stdio> 10 --out_peaklist='$averageFragSpectra_output_tsv'
14 <exit_code range="1:" /> 11 --pa='$pa'
15 </stdio>
16 <command interpreter="Rscript"><![CDATA[
17 averageFragSpectra.R
18 --out_rdata="$averageFragSpectra_output_rdata"
19 --out_peaklist="$averageFragSpectra_output_tsv"
20 --pa="$pa"
21 --av_level=$av_level 12 --av_level=$av_level
22 --cores=\${GALAXY_SLOTS:-4} 13 --cores=\${GALAXY_SLOTS:-4}
23 --minfrac=$minfrac 14 --minfrac=$minfrac
24 --minnum=$minnum 15 --minnum=$minnum
25 --ppm=$ppm 16 --ppm=$ppm
28 --av=$av 19 --av=$av
29 $sumi 20 $sumi
30 $rmp 21 $rmp
31 ]]></command> 22 ]]></command>
32 <inputs> 23 <inputs>
33 <param name="pa" type="data" label="purityA object" format="rdata" 24 <param argument="--pa" type="data" label="purityA object" format="rdata"
34 help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/> 25 help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/>
35 26
36 27
37 <param name="av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help=""> 28 <param argument="--av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
38 <option value="intra" selected="true">within a MS data file</option> 29 <option value="intra" selected="true">within a MS data file</option>
39 <option value="inter">across MS data files</option> 30 <option value="inter">across MS data files</option>
40 <option value="all">within and across MS data files (ignoring intra and inter relationships)</option> 31 <option value="all">within and across MS data files (ignoring intra and inter relationships)</option>
41 </param> 32 </param>
42 33
43 34
44 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" /> 35 <param argument="--snr" type="float" min="0.0" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
45 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" /> 36 <param argument="--ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
46 <param name="minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" /> 37 <param argument="--minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" />
47 <param name="minnum" type="integer" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" /> 38 <param argument="--minnum" type="integer" min="1" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" />
48 <param name="ppm" type="float" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." /> 39 <param argument="--ppm" type="float" min="0.0" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." />
49 <param name="sumi" type="boolean" checked="false" truevalue="--sumi" falsevalue="" label="Sum intensities across (averaged) scans?" help="" /> 40 <param argument="--sumi" type="boolean" checked="false" truevalue="--sumi" falsevalue="" label="Sum intensities across (averaged) scans?" help="" />
50 <param name="av" type="select" label="Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering." help="This is ignored for intensities when intensities are summed." > 41 <param argument="--av" type="select" label="Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering." help="This is ignored for intensities when intensities are summed." >
51 <option value="median" selected="true">median</option> 42 <option value="median" selected="true">median</option>
52 <option value="mean">mean</option> 43 <option value="mean">mean</option>
53 </param> 44 </param>
54 45
55 <param name="rmp" type="boolean" checked="true" truevalue="--rmp" falsevalue="" label="Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead." 46 <param argument="--rmp" type="boolean" checked="true" truevalue="--rmp" falsevalue="" label="Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead."
56 help="" /> 47 help="" />
57 </inputs> 48 </inputs>
58 <outputs> 49 <outputs>
59 <data name="averageFragSpectra_output_rdata" format="rdata" label="${tool.name} (${av_level}) on ${on_string}: RData" /> 50 <data name="averageFragSpectra_output_rdata" format="rdata" label="${tool.name} (${av_level}) on ${on_string}: RData" />
60 <data name="averageFragSpectra_output_tsv" format="tsv" label="${tool.name} (${av_level}) on ${on_string}: peaklist" /> 51 <data name="averageFragSpectra_output_tsv" format="tsv" label="${tool.name} (${av_level}) on ${on_string}: peaklist" />